Hello Everyone
There's probably an easy way to do this, but I haven't found it.
I've refined a 1.1 A structure with refmac and want to inspect the thermal
ellipsoids. Specifically I want to know if any of them are non-positive
definite and I want to know which have very large anisotropy. (I ca
A metaserver such as bioinfobank is helpful if your sequence is not
super-secret, especially if one is not an experienced modeller.
http://meta.bioinfo.pl/submit_wizard.pl
It submits your sequence to a range of sequence-based and threading-
based servers. Models (c-alpha, built with modell
My preference is also for the full structure factor amplitude. I
would have said that I'd never seen the term structure amplitude used.
However, I just looked this up in my old Stout & Jensen (1968 edition
- brown cover) and find that (on p. 195) where |F| is introduced they
define it as:
le methods (software?) is out there for,
perhaps, data reduction (if there is such a thing for fiber
diffraction) or subsequent analysis.
Thanks,
Sue
Sue Roberts
Department of Biochemistry & Molecular Biophysics
University of Arizona
[EMAIL PROTECTED]520 621-8171
Hello
I wish to thank everyone for all the helpful replies. A summary
follows:
While some expressed surprise at the zinc lability, others related
tales of difficulty keeping zinc in a protein.
Suggested ways of overcoming the problem included:
1) Use of TCEP as a reducing agent
2)
Hello Everyone
I've been trying to crystallize a zinc-containing enzyme for what
seems to me to be an eternity. The protein contains stoichiometric
zinc (1 zinc/ protein monomer) when isolated and the zinc is required
for activity. Each crystal we've obtained has lost the zinc and
conta
I don't think the term "high resolution" has any real definition or
meaning anymore. If you're proud of the resolution, put the number in
the title of the paper and let the reader decide. At one time 2 A was
high resolution, but I wouldn't consider that high resolution today
for a plain v
vailable from both ends (phenix, ccp4) to easily
go from
partial to total and back. The rest is the matter of personal
preferences.
Cheers,
Pavel.
---
Pavel V. Afonine, Ph.D.
Lawrence Berkeley National Lab, Berkeley CA, USA (http://
www.lbl.gov/)
CCI: Computational Crystallography Initiat
le that folder names can't begin with periods.
> I am getting the impression that CCP4 is buggy on OS X. Any
> information on avoiding these problems and getting CCP4 to work?
>
> Thank You,
> Kurt Padilla
>
> on the behalf of:
>
> Kathleen Frey
> Amy Anderson
quality, and R-work and R-free will diverge to some extend due to
this. If you force the copies to be identical, the R-work & R-free
will still be different due to observational errors. In both
cases, however, the R-free will be very close to the R-work.
Sue Roberts
Biochemistr
..
Many thanks
Kristof
--
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327477
--
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
Sue Roberts
Biochemistry & Bio
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.467.4049
cel: 773.608.9185
email: [EMAIL PROTECTED]
***
Sue Roberts
Biochemistry & Biophysics
U
ctual opinions, living or dead, is purely coincidental.
**********
Sue Roberts
Biochemistry & Biophysics
University of Arizona
[EMAIL PROTECTED]
r Protein Research, Osaka University
3-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN
Tel: +81-6-6879-8634
Fax: +81-6-6879-8636
Sue Roberts
Biochemistry & Biophysics
University of Arizona
[EMAIL PROTECTED]
ed by the pdb in the
last year with resolution > 1.1 A and found at least one with the
same problems (I stopped looking after I'd found one).
Sue
Sue Roberts
Biochemistry & Biopphysics
University of Arizona
[EMAIL PROTECTED]
data, especially in terms of the
Rmerge and sigma cuttoff.
Thanks in advance,
*Shane Atwell*
Sue Roberts
Biochemistry & Biopphysics
University of Arizona
[EMAIL PROTECTED]
detected with sfcheck - we
hadn't yet figured that out when I posted the message.] A run
through the anisotropy server at UCLA
http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/
has unstuck the refinement and made the maps much more pleasing.
Sue
Sue Roberts
Biochemistry & Biopphysics
U
s a failed
refinement). (My bias is that such data sets are almost never
twinned and one should look elsewhere for the problem, but perhaps
others know better.)
Sue
Sue Roberts
Biochemistry & Biopphysics
University of Arizona
[EMAIL PROTECTED]
FFT
#!/bin/sh
set -e
fft hklin model.mtz mapout fofc_f.map <_
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Sue Roberts
Biochemistry & Biopphysics
University of Arizona
[EMAIL PROTECTED]
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